My Firefox chrome (the menus and such) is set up like this: My the book mark items that are normally on the Bookmark bar are moved to be next to the File/Edit menus. The bookmark bar is hidden. I also have removed the search bar, since I used smart keywords.
About half the time I open a new window, or restart Firefox, the book marks are gone, and the search bar comes back next to the address bar.
I am currently running Firefox 3.5.4 on Ubuntu 9.10, but I have seen this behavior in the past on Firefox 3.0 and Windows 7, Windows XP and Ubuntu 9.04.
This is a long time problem, that I cam quite frustrated with.